Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins

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• 作者：Ian R. Craig ; Christopher Pfleger ; Holger Gohlke ; Jonathan W. Essex ; Katrin Spiegel
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2011
• 出版时间：October 24, 2011
• 年：2011
• 卷：51
• 期：10
• 页码：2666-2679
• 全文大小：1302K
• 年卷期：v.51,no.10(October 24, 2011)
• ISSN：1549-960X

文摘

The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer^PCA, which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer^PCA approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer^PCA for rationalizing and improving the understanding of the molecular basis of protein鈥搇igand interaction and bioactivity. A Python program implementing the PocketAnalyzer^PCA approach is available for download under an open-source license (http://sourceforge.net/projects/papca/ or http://cpclab.uni-duesseldorf.de/downloads).